Featrue Request: Display of structural variants similarly to Pacific Biosciences "BridgeMapper" Protocol

[boykebunk]

For long read data, Pacific Biosciences developed a great visualization technique named BridgeMapper (http://files.pacb.com/software/smrtanalysis/2.3.0/doc/smrtview/help/Webhelp/App_View_Epipro.htm). However, the development of this visualization has been discontinued although very helpful for inspection of all types of long read assemblies.

Briefly, a contig-wise color code was established and reads were shown, which have a supplementary/secondary alignments. Those reads are being color coded according to the position where their supplementary/secondary alignment occur.

For genome assemblies this allows for retrieval of possible connections of WGS contigs to combine them, identify misassembled contigs and even reveal potential heterogenous structural variants.

[jrobinso]

@boykebunk Thanks for posting this, I will look into it. I don't understand reference "supplementary/secondary" alignments, those are fundamentally different things. Supplementary alignments == split reads or chimeric alignments, primary/secondary refer to ambiguously aligned reads (could align to multiple locations). This is always a source of confusion.

[boykebunk]

Thanks for clarification! As we are talking about split mapped reads supplementary alignments should be correct then.

[amwenger]

@boykebunk - Would https://github.com/igvteam/igv/issues/731 address your needs? That issue suggests to color the ends of clipped alignments based on the distance to and relative orientation of alignments of adjacent parts of the read. It includes a suggestion to use a color that indicates contig when the next part of the read aligns to a different contig.

[boykebunk]

Hi Aaron, Yes, I had a look to #731. I had a look into the pseudocode and

Inter-chromosomal translocation If A.chrom is different than B.chrom: Return color used for the other chromosome

adresses the needs.